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- PDB-7kch: Myosin XI-F-actin complex -

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Basic information

Entry
Database: PDB / ID: 7kch
TitleMyosin XI-F-actin complex
Components
  • Actin, alpha skeletal muscle
  • Unconventional myosin heavy chain
KeywordsCONTRACTILE PROTEIN / myosin / actin / cytoskeleton / motor protein
Function / homology
Function and homology information


Striated Muscle Contraction / myosin complex / cytoskeletal motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...Striated Muscle Contraction / myosin complex / cytoskeletal motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / hydrolase activity / calmodulin binding / ATP binding
Similarity search - Function
Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain ...Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Unconventional myosin heavy chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
Chara corallina (plant)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsGong, R. / Alushin, G.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM114627 United States
CitationJournal: Nat Chem Biol / Year: 2021
Title: Optical control of fast and processive engineered myosins in vitro and in living cells.
Authors: Paul V Ruijgrok / Rajarshi P Ghosh / Sasha Zemsky / Muneaki Nakamura / Rui Gong / Lin Ning / Robert Chen / Vipul T Vachharajani / Alexander E Chu / Namrata Anand / Raphael R Eguchi / Po-Ssu ...Authors: Paul V Ruijgrok / Rajarshi P Ghosh / Sasha Zemsky / Muneaki Nakamura / Rui Gong / Lin Ning / Robert Chen / Vipul T Vachharajani / Alexander E Chu / Namrata Anand / Raphael R Eguchi / Po-Ssu Huang / Michael Z Lin / Gregory M Alushin / Jan T Liphardt / Zev Bryant /
Abstract: Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. ...Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
History
DepositionOct 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
G: Actin, alpha skeletal muscle
A: Unconventional myosin heavy chain
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,66110
Polymers209,3064
Non-polymers1,3556
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACTA1, ACTA / Production host: Gallus gallus (chicken) / References: UniProt: P68139
#2: Protein Unconventional myosin heavy chain


Mass: 83015.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chara corallina (plant) / Gene: ccm
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q9SSU1
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Myosin XI-F-actin complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 209 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Gallus gallus (chicken)9031
21Chara corallina (plant)43696
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Gallus gallus (chicken)9031
21Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)1491790
Buffer solutionpH: 7
Details: 10 mM imidazole pH 7.0,50 mM KCl,1mM MgCl2, 1mM EGTA, 0.5 mM DTT, 0.01% NaN3
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMImidazoleC3N2H41
250 mMPotassium chlorideKCl1
31 mMMagnesium chlorideMgCl21
41 mMEGTAC14H24N2O101
50.5 mMDTTC4H10O2S21
60.01 weight/volumesodium azideNaN31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: -4000 nm / Nominal defocus min: -1000 nm / Cs: 0 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 67.12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2Leginonimage acquisition
4CTFFIND4.1CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -167.11 ° / Axial rise/subunit: 27.45 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 70000
3D reconstructionResolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45779 / Algorithm: FOURIER SPACE / Num. of class averages: 23 / Symmetry type: HELICAL

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